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Background Chinese cordyceps (Lepidoptera: Ophiocordyceps sinensis)is a larval-fungus complex. The concentration and distribution of arsenic (As) may vary during the stroma (ST) germination process and between the sclerotium (SC) and the ST. The soil-to-Chinese cordyceps system is an environmental arsenic exposure pathway for humans. We studied the As concentration in the soil, the SC, and the ST of Chinese cordyceps, and performed a risk assessment. Methods Soil and Chinese cordyceps samples were collected from the Tibetan Plateau in China. The samples were analyzed for the total As concentration and As species determination, which were conducted by inductively coupled plasma mass spectrometry (ICP-MS) and HPLC-ICP-MS, respectively. Results The concentration of total As in the soil was much higher than in SC and ST. The major As species in the soil was inorganic AsV. In SC and ST, organic As was predominant, and the majority of As was an unknown organic form. There are significant differences in the As distribution and composition in soil, SC, and ST. Our risk assessment indicated that chronic daily ingestion was higher than inhalation and dermal exposure in children and adults. The hazard index (HI) of the non-carcinogenic and cancer risks (CR) for human health were HI ≤ 1 and CR −4, respectively. Conclusion The Chinese cordyceps possesses highly-efficient detoxifying characteristics and has a significant role in As transformation during its life cycle. We found that the levels of As in soils from the habitat of Chinese cordyceps were higher than the soil background values in China, but the probability for incurring health risks remained within the acceptable levels for humans.